Thursday, November 9, 2017

The Evolution Of Cooperation

Biology concepts – biological timeline, serial endosymbiosis, endocystosis, evolution


Taxonomy, the placing of species in different
groups based on their characteristics, changes
everyday – literally everyday – organisms are
placed in different groups and groups are created
and eliminated. That better be a temporary tattoo!
If we look at the 3.5 billion year history of life on Earth, we see that out planet was lifeless for almost a quarter of its span, and animals have been around just a short blip of time, a mere 760 million years. Often, it seems that the big numbers to get in the way of understanding the time line as a whole.

If we treat the entire history of earth as one year, we might get a clearer picture. Earth coalesces from space dust on January 1st, but it isn’t until March 22nd that we find the first evidence of life. These most primitive fossils are of the prokaryotes called Archaea (Greek for “ancient”). Not long after this, maybe a week or so, the eubacteria and Archaea separate from one another.

Then we have to wait until August 7th to find a big change; the first eukaryotic organisms are seen. These represent a fundamental change in the organisms, having nuclei and membrane bound organelles. It's amazing that we must travel 3/4 through our one year time line before we see a cell that looks somewhat like ours!


Here is one of the Namibia sponge fossils recently
discovered in Africa. It represents the oldest animal
in the fossil record. Just how that was recognized as a
fossil is beyond me – I think I have six of those in my
garden!
Later in the year, around October 30th at noon, we see the first animals. Fossils of Namibia sponges in Africa were first reported in February of 2012. This fossils are 100 million years older than the previously oldest animal remains, so our new data means that animals have been around for an additional week in our time line of a year.

Insects appear about Nov. 26th, while mammals first show up around Dec. 8th. The dinosaurs became extinct sometime in the afternoon of Dec. 26th, so they had very little time to play with their Christmas presents. Homo sapiens (us) didn’t appear on the doorstep looking for holiday cheer until 11:40 pm on New Years Eve, Dec. 31st!

Our time line analogy shows us that prokaryotes are the wise old ancestors; we aren’t even old enough to be rebellious teenagers, although we still think we know everything. The key question is: how did we progress to analogy-makers from single celled Archaea? If we put together several of the topics we have been discussing in the past three weeks, we may come up with an interesting step in the process. Our clues include:

1) Microcompartments exist in bacteria, like organelles, and they also exist in eukaryotic cells, especially in nucleus' function. This links eukaryotes to prokaryotes.

2) Sometimes cells will engulf objects, parts of other cells, or other cells. Depending on the size of the particle or cell, we may call this endocytosis or phagocytosis, and is similar to how we saw keratinocytes take up melanosomes.

3) Three eukaryotic organelles, the nucleus, the mitochondria, and the chloroplast have double membranes, and they each have their own DNA.

4) There are two different types of prokaryotes, archaea and bacteria.

Bacterial microcompartments give prokaryotes some compartmentalization in order to carry out necessary chemical reactions. Eukaryotes also have some prokaryotic microcompartment remnants, like the nuclear vault complex. This shows crossover between prokaryotes and eukaryotes, and gives us clues about eukaryotic origins. In fact, the currently accepted theory about the evolution of organelles - the very thing that makes cells eukaryotic - has to do with both types of prokaryotes - archaea and bacteria.


There are three types of endocytosis (with exceptions).
Endocystosis of large objects and cells is called phagocytosis.
Internalization of very small molecules and fluid is called
pinocytosis. Other molecules of various sizes have specific
receptors that recognize them on the cell surface. They are
brought in by receptor-mediated endocytosis. Notice that no
matter what method is used, the internalized particle ends up
surrounded by part of the cell membrane.
The key to their interrelationship has to do with endocytosis (endo = into, cyto = cell). Most prokaryotic and eukaryotic cells eat other cells; they do it all the time – it is how heterotrophic organisms (those that can't make their own carbohydrates, ie. non-plants) gain their nutrients. We do it too, just on a larger scale; we eat millions of cells at a time; often these millions of cells can take the shape of a steak or a carrot.

When a cell, protein, other molecule is engulfed by another cell, it is wrapped in a portion of the aggressor cell’s membrane. The naked molecule is now contained in a vesicle, a membrane bound sac, like the melanosome. If the endocytosed material is an entire cell, something that has its own membrane, then it ends up with two membranes, just like the mitochondrion, chloroplast, and nucleus.

Most often, when one prokaryote phagocytoses another, the story is over….gulp, yum, digest. But scientists believe that long ago (sometime in the first week of August in our time line) an endocytosed cell did not go gentle into that good night. Instead, it took up residence in the cell that ate it. In this rare case, it turned out that both cells gained from the situation.

The endocytosed cell was protected from other predators and had a ready supply of nutrients from the parent cell. The captured cell made lots of ATP, but it didn’t need much because it was being supplied with everything it needed; it didn't need to make energy to move or hunt or escape. Most of its ATP production went unused. Perhaps it moved this excess ATP out into the parent cell. So the parent cell gained a source of ATP production. This was mutualism, a type of symbiosis in which both parties benefit.


Clownfish clean the sea anemone and keep it
parasite free. The poisonous anemone provides
a safe environment for the clown fish; no
unwanted house guests! This is a good example of
mutualistic symbiosis. Bet you didn’t know you
learned things from Finding Nemo.
Imagine if the same thing happened with a cyanobacterium, a cell that could perform photosynthesis. The same sort of symbiosis might be set up, with the endocystosed cell providing carbohydrates and the parent cell providing protection.

Now imagine that these captured cells, the photosynthesizer and the ATP maker, replicated themselves inside their parent cells just as they would if they were outside, living on their own. They could easily do this since they still retained their own DNA and cell division mechanisms.

This is in fact what scientists believe happened. The endocytosed cells that produced extra ATP evolved into our mitochondria. Endocytosed cells that could do photosynthesis became the chloroplasts of plants. Not all cells are plants because not all cells with an ancestral mitochondria also ate a cyanobacterium. The fact that plants cells have mitochondria as well as chloroplasts tells us that plant cells developed AFTER cells with mitochondrial ancestors.

But the nucleus may be a tougher nut to crack. It may be that an endocytosed cell good at keeping DNA safe and producing ribosomes became the nucleus, by endocytosis. The data suggests that our DNA is closer to archaeal DNA than bacterial DNA, so it would have been a eubacteria endocytosing an archaea. Or perhaps the archaea invaded the bacterium rather than being endocytosed. The nucleus does have a double membrane and uses some prokaryotic microcompartments to this day, so this could make sense.

But other theories also exist, including one that says an intermediate eukaryotic cell, theoretically called a chronocyte, had developed some organelles on its own or by endocytosis, including a cytoskeleton. This internal structure allowed the cell become bigger, and engulf a cell large enough to evolve into the nucleus.

Another theory uses an evolutionary exception as its basis. Some aquatic bacteria, called planctomycetes (planktos = drifting and mycete = fungus-like), have an organized interior, with something that looks like a nucleus with pores, called a nucleoid. In fact, when they were first discovered, planctomycetes were mistaken for small fungal cells. However, we know they are prokaryotes by DNA sequencing. I thought prokaryotes didn’t have nuclei! Remember that in biology, there is almost always an exception. The planctomycete nucleoid structure suggests that the nucleus may have evolved on its own, without endocytosis.


The planctomycete species, Pirellula (latin for small pear),
is an exceptional bacterium. It has a primitive nucleus
and a stalk that makes it look like a eukaryotic
fungal cell. It was misidentified for a long time, and is
a prime example of why the tattoo above was a bad
idea!
Finally, another theory posits that the nucleus originated from a virus infecting a primitive prokaryote, and this internalized virus forming a nucleus or causing the cell to be predated by another cell. Even though there are different theories for the nucleus, we can see that the three organelles that have double membranes look like they could have been endocytosed cells, that then evolved into the organelles we see today. Endocytosis resulted in symbiosis, so the theory of organelle development is called endosymbiosis.

Endosymbiosis is a cool idea and has lots of support. Besides the double membrane evidence, lets look at how dividing cells get more mitochondria and chloroplasts. These organelles replicate on their own by binary fission, just like bacteria. They can replicate on their own because they have their own DNA. Mitochondrial DNA (mtDNA) and chloroplast DNA (chDNA) are smaller pieces of DNA than nuclear chromosomes, mtDNA and chDNA look much like the small genomes of bacteria. They are also circular pieces of DNA, not linear like our nuclear chromosomes.

By replicating through binary fission, they can be portioned in the dividing cell so that each daughter gets some of these crucial organelles. But it isn’t as if mitochondria and chloroplasts of today look just like the engulfed ancestors. Mitochondrial and chloroplast genomes are greatly reduced from what they used to be.


Serial endocytosis is also called secondary (2˚) endocytosis.
This refers to the movement of DNA from internalized
cells to the nucleus of the endocytosing cell by lateral
gene transfer. This strengthens the symbiotic relationship
between the two organisms until they can be considered
one total organism.
The mitochondria only codes for about thirteen proteins, just enough for it to replicate on its own. The DNA that codes for the rest of the 1500 or so proteins needed for mitochondrial function have been transferred to the nucleus over time. For a discussion of the chloroplast and its horizontal gene transfer to the nucleus, see the posts on C. litorea, the photosynthetic sea slug.

We know that these gene transfers were actual events based on the structure and nucleotide ordering of the mitochondrial and photosynthetic sequences in the eukaryotic chromosomes; they are structured and coded in ways that are typically bacterial. Because of this slow transfer of DNA to the nucleus, endosymbiosis has evolved over time, changing again and again until we got today’s organelles. Therefore, our idea of organelle development is sometimes called serial endosymbiosis theory (SET), because it must have had several different changes through evolution.

Now that we have laid out the evidence and sense for the serial endosymbiosis theory, next week we can talk about some exceptions that show us that that some organisms just can't stick with something that seems to work. Some life just has to take the road less traveled.



Okie JG, Smith VH, & Martin-Cereceda M (2016). Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts. Proceedings. Biological sciences / The Royal Society, 283 (1831) PMID: 27194700

Kostygov AY, Dobáková E, Grybchuk-Ieremenko A, Váhala D, Maslov DA, Votýpka J, Lukeš J, & Yurchenko V (2016). Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action. mBio, 7 (2) PMID: 26980834

Erbilgin O, McDonald KL, & Kerfeld CA (2014). Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Applied and environmental microbiology, 80 (7), 2193-205 PMID: 24487526



For more information or classroom activities on history of life time lines, endocytosis,  serial endosymbiosis theory, evolution of eukaryotes, or planctomycetes, see:

History of life on Earth timelines -

Endocytosis –

Serial endosymbiosis theory –

Evolution of eukaryotes –

Planctomycetes –